Hi! How can I use DESeq2 to analyze my RIP-seq data, which includes both INPUT and IgG control samples for each of the three replicates across two conditions: treated and untreated? Is it correct to put all the samples together, considering IP, INPUT, and IgG as different assays, and use the following formula?

dds <- DESeqDataSetFromMatrix(countData = count_matrix,
                              colData = colData_df,
                              design = ~ assay + treat + assay:treat)
dds <- DESeq(dds, test="LRT", reduced= ~ assay + treat)

And is it correct to retrive the results in this way?

results(dds, contrast=list("assayIP.treatTREATED", "assayigG_ctrl.treatTREATED"))

Thanks in advance,

AT

You are mixing two threads of advice (I guess from different support site posts).

You can just do the LRT then:

results(dds)

This gives you the LRT result.

The other code you have posted is for a different setup.

And just to link to a relevant thread:

DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)